Week 13 Diversity Of Marine Microbes Flashcards
Why is SSU ribosomal RNA an ideal chronometer?
- Present in all organisms
- Slow mutation rate
- Performs an identical function in all organisms
What can be used to compare the phylogeny of close and distinct taxa?
Nucleotide or inferred amino acid sequence
What is ARB-Silva?
The biggest database of SSU and LSU rRNA
How were bacterial/archaeal species operationally defined in teh past?
- Distinctive phenotype property
2. Genomically coherent - DNA-DNA HYBRIDISATION >70%
Using 16S rRNA gene sequencing, what is the definition of a species?
> 97%
Using whole genome sequencing what is the definition of a species?
95-96% average nucleotide identity
What is a candidates species>
Uncultured bacteria that cannot be assigned to a valid species because we do not have the full information about their phenotype
What is an operational taxonomic unit
Sequences grouped on the basis of similarity - without saying for sure if its a species
What are amplicon sequence variants?
Sequences that aren’t grouped
What happens when you use whole genome sequencing instead of 16S rRNA sequencing to define a species?
Some of the positions of microbes have been further shifted
What does this image show? (2 things)
- Bacteria is highly diverse
2. There are significant differences between pelagic and benthic microbes
What are the most numerically abundant bacteria?
Proteobacteria
Name at least three common marine bacteria?
- Cyanobacteria
- Bacteroidetes
- Actinobacteria
- Chloroflexi
What are a-proteobacteria?
Metabolic generalists
What is the most common bacterial species in the ocean?
A-proteobacteria - SARS 11
What are b-proteobacteria a part of?
Y-proteobacteria
What 3 main functions do y-proteobacteria have?
- POC mineralises
- Oxidation of ammonia
- Oxidation of methane
- Oxidation of sulphide
What are planctomycetes associated with?
Marine snow and an anammox bacteria
Many bacteroidetes and planctocytes harbour taxa that have what function?
Degradation of complex organic compounds
Marine archaea were long believed to be thermophiles, what have they also been discovered to be?
Living mesophillic lifestyles
How much abundance does marine archaea have in the twilight zone?
Up to 40%
What can Marine Group 1 do that was thought to only be in proteobacteria?
Ammonia oxidising
What important function does crenarchaeota have?
Chemolithoautotrophic through sulphur reduction
What other roles do archaea have in recycling?
Roles in methane and nitrogen cycling
